Along with the industrial and biological importance of peroxidase

Along with the industrial and biological importance of peroxidases, together with the availability of fully sequenced fungal genomes, a genomics resource is required for better understanding of peroxidases

at the genome-level. Peroxidase genes might be identified by using domain prediction tools, such as InterPro scan [21] or Pfam [22]. However, identification based on domain profiles could result in false positives. For example, NoxA [23] and a metalloreductase (FREA) [24] in Aspergillus nidulans showed the same domain profiles predicted by InterPro scan [21] and Pfam [22]. Since ferric reductases (FRE) and ferric-chelate reductases (FRO) share high structural Seliciclib price similarity with Nox [25], the gene encoding FREA would become a false positive in domain-based prediction of Nox genes. Because filtering out false positives is an important issue in studying comparative or evolutionary genomics on Nox genes, Nox family is divided into three subselleck families, NoxA, NoxB, and NoxC. Previously, a database named as PeroxiBase [26] was developed to archive the genes encoding peroxidases in a wide range of taxonomy.

Although PeroxiBase contains fungal peroxidases, it does not specifically focus on fungi and archive genes encoding NoxR, which are known to regulate NoxA and NoxB AZD5582 mw in fungi [27–29]. Hence, it is necessary to build a peroxidase database for comparative and evolutionary analysis in fungi. Here, we developed a new web-based fungal peroxidase

database (fPoxDB; http://​peroxidase.​riceblast.​snu.​ac.​kr/​) to provide a fungi-oriented archive with manually improved catalogue of Nox genes and to support comparative ADAMTS5 and evolutionary genomics of genes encoding various peroxidases. Finally, we show an overview of the taxonomic distribution of peroxidase genes in the kingdom Fungi which could be applied for investigation of phylogenetic relationship. Construction and content Construction of the pipeline for identification of the genes encoding peroxidases In order to set up a pipeline for fPoxDB, the protein sequences of fungal peroxidases were retrieved from PeroxiBase [26]. Particularly, the gene family “Ancestral NADPH oxidase” was redefined with three gene families, NoxA, NoxB, and NoxC. Protein sequences of two other NADPH oxidase families, Duox (dual oxidase), and Rboh (respiratory burst oxidase homologue), were also included. Majority of Duox and Rboh were found in animals and plants, respectively. They were integrated into fPoxDB to detect their remote homologues in fungi. In addition, protein sequences of NoxR, the regulatory subunit of NoxA and NoxB, were collected from various literatures. The protein sequences for each gene family were subjected to multiple sequence alignment by using T-Coffee [30], then manually curated and trimmed for refinement.

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